Heat Transport and Phonons

Heat Transport

The save options are --save (figure) and --save-data (processed data); the older forms save and save_data are still accepted.

For emd, nemd, and hnemd, a missing model.xyz is generated automatically from an existing legacy xyz.in. For nemd/hnemd, scale_eff_size accepts a number or a safe arithmetic expression such as '100/2'. Optional --quantum (legacy quantum) adds a quantum-corrected SHC spectrum using the temperature from run.in; it requires shc.out.

emd (plt_emd.py)

Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).

Input Files: EMD output files from GPUMD

gpumdkit.sh -plt emd x --save-data        # export processed data
gpumdkit.sh -plt emd x --save --save-data # save the figure and data

--save saves the figure as emd.png. --save-data saves the processed arrays as data_emd.npz and tab-separated data_emd.txt; the two options are independent.

emd2 (plt_emd2.py)

Plots heat-current correlation and total EMD thermal conductivity in the x, y, and z directions in one figure. It uses the same run.in and hac.out files and averaging rule as plt_emd.py.

Input Files: EMD output files from GPUMD

gpumdkit.sh -plt emd2             # Display all directional results
gpumdkit.sh -plt emd2 save        # Save as emd2.png

The HAC panels use a logarithmic correlation-time axis and retain the signed HAC values on the y-axis. A physically zero direction is shown as a zero curve. The reported uncertainty follows the legacy half-window spread divided by the square root of the number of HAC repeats; it is not an independent- trajectory standard error.

nemd (plt_nemd.py)

Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.

Input Files: NEMD output files from GPUMD

Parameters:

gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [--save] [--save-data] [--quantum]
gpumdkit.sh -plt nemd --save-data                         # use defaults and export data
gpumdkit.sh -plt nemd Auto 1 60 --save --save-data       # save the figure and data

NEMD writes NPZ and TXT data only with --save-data; neither is written by default. This option is independent of --save.

hnemd (plt_hnemd.py)

Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.

Input Files: HNEMD output files from GPUMD

Parameters:

gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [--save] [--save-data] [--quantum]
gpumdkit.sh -plt hnemd --save-data             # use defaults and export data
gpumdkit.sh -plt hnemd 1 60 --save --save-data # save the figure and data

viscosity (plt_viscosity.py)

Plots the stress autocorrelation and viscosity components from viscosity.out, including diagonal and off-diagonal components.

Input Files: viscosity.out from the GPUMD viscosity calculation

gpumdkit.sh -plt viscosity

Phonons

phonon (plt_phonon.py)

Plots a phonon band structure generated by calculator 414. The plotter reads the q-point path and high-symmetry labels directly from a line-mode QPOINTS file, so the path does not need to be repeated in the plotting script.

Input Files: A phonon data file (default phonon_NEP.dat) and QPOINTS

The calculation step is interactive:

gpumdkit.sh -> 4) Calculators -> 414) Calc phonon band structure

The Python prompts accept a primitive-cell structure (default PRIMCELL.vasp), a NEP model (default nep.txt), a line-mode path (default QPOINTS), the supercell, the displacement amplitude, and the output name (default phonon_NEP.dat). The calculation requires phonopy in addition to the usual GPUMDkit/Calorine dependencies.

Plot the result with:

gpumdkit.sh -plt phonon
gpumdkit.sh -plt phonon phonon_DFT.dat
gpumdkit.sh -plt phonon phonon_NEP.dat QPOINTS save

The phonon data file is optional. If it is omitted, the plotter reads phonon_NEP.dat; if only one file is supplied, the path file defaults to QPOINTS.

phonon_comp (plt_phonon_comp.py)

Compares two or more phonon band-structure files. The legend is inferred from the filename: phonon_NEP.dat becomes NEP, phonon_DFT.dat becomes DFT, and phonon_MACE.dat becomes MACE.

gpumdkit.sh -plt phonon_comp phonon_DFT.dat phonon_NEP.dat save
gpumdkit.sh -plt phonon_comp phonon_DFT.dat phonon_NEP.dat phonon_MACE.dat \
    --qpoints QPOINTS save

The default path file is QPOINTS; use --qpoints FILE for another one. All files must use the same q-point sampling and the same number of bands.

pdos (plt_pdos.py)

Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).

Input Files: model.xyz, run.in, dos.out, mvac.out

gpumdkit.sh -plt pdos
gpumdkit.sh -plt pdos save

Heat capacity output: